Toilet, for the running i would suggest running at least 4 k without stopping, unless you are trying to shed some pounds. I can only speak from my experience as an "in shape" guy but with terrible cardio. About 2 months ago i started running, and it was tough for me to do 2 k without huffing and puffing. I just kept running, and didn't worry about the pace (although a good pace came very quickly.) Seriously, after like 3 weeks i was able to run 5k, and now i can do 10k, although it takes me 50 minutes. My 2.4 started at 12 minutes 2 months ago, and i did it this week at 9:35. I would suggest doing something like running as hard as you can for 3 minutes and walking/jogging for 3 minutes and repeating that at least 3 times. Thats what i did once a week right when i started, and it was pure hell. But my cardio increased dramatically. Plus, i smoke, so if you don't, you could probably blow these times away.
As for the walking with wieght in a back pack and getting the feet tough, i think i want to just experience that at basic. Maybe it sounds crazy but i want to struggle through that sort of pain and come out the other side tougher. Blisters will suck, and the ruck march will be tough, but whatever, pain is only temporary. (Maybing ill be wishing i prepared for those things before i left but i don't think i will.)